Difference between revisions of "Add a Part to the Registry"

 
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<TABLE width='827px' border='0' cellspacing='0' cellpadding='0' style='border: none;'><TR><TD nowrap width='30%' style='padding-right: 2em;text-align: left;'><SPAN style='font-size: 200%; line-height: 200%'>Add a Part to the Registry</SPAN><TD align='center'><TD width='30%' align='right'></TABLE><TABLE width='817px' border='0' cellspacing='0' cellpadding='0' style='margin-left: 10px;background-color: white; padding-left: 10px;line-height: 150%; ' >
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{{HelpPage/MainLinks}}
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<TR><TD colspan='9'width='100%' style='height: 1px; background-color: gray;'><TR><TD colspan='9' style='padding-top: 10px;'>Members of Registry groups may add three kinds of parts to the registry:
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__NOTOC__
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Basic Parts, Composite Parts, and Construction Intermediates.<TR><TH align='left' width='25%'>Basic Parts
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Members of iGEM teams and labs can add two kinds of parts to the Registry: '''Basic Parts''' and '''Composite Parts'''.
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                <TH align='left'><A href='add_part_b.cgi'>Add a Basic Part Now...</A><TR><TD colspan='9' style='padding-left: 15px'>
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Basic Parts are atomic units of DNA. They are not assembled
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from other parts in the Registry. The design for a basic part must specify the exact sequence of the part, provide
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'''The most important feature of a standard biological part should be that a user of the part does not have to talk to the part's designer. This is achieved by completely documenting the part.'''
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annotation of that sequence, and design notes about the sequence itself. The DNA for a basic part may be obtained by
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de-novo synthesis, by primer extension and PCR, or other microbiological techniques. Like all parts, a Basic Part is stored
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in a plasmid, surrounded by a restriction-enzyme cloning region. This cloning region is not included in the sequence of the
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Parts '''must''' have a DNA sequence. Registry users should [[Help:Document_Parts|document]], model, characterize, and measure their parts, and provide that information on their [[Help:Nav/Part_Main_Page|part pages]].
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part. It can be provided by the Registry software.<TR><TH align='left' width='25%' style='padding-top: 10px;'>Composite Parts
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                <TH align='left'><A href='add_part_c.cgi'>Add a Composite Part Now...</A><TR><TD colspan='9' style='padding-left: 15px'>
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A part can be identified by its DNA sequence, and may be compatible with several [[Help:Assembly_Compatibility|Assembly Standards]]. A <strong>sample</strong> of a part may be stored in a plasmid backbone that dictates assembly (ex. [[Part:pSB1C3|pSB1C3]]), and flanked by the [[Help:Prefix-Suffix|prefix and suffix]]. The prefix and suffix are ''never'' included in the sequence of the part when documented on the Registry, as they are a product of the plasmid backbone, and not the part itself. '''Sample submission of parts is no longer a requirement for the iGEM competition.'''
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Composite Parts are made from an ordered list of basic parts or other
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composite parts. An explicit sequence of DNA cannot be included in the list, but should first be added to the Registry
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{{AssemblyStandards/Accepted}}
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as a basic part. The Registry maintains the list of subparts given by the designer as primary documentation of a composite
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<br />
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part. The Registry software also provides a list of all the basic parts that make up the composite part. This is called the
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deep parts list and is used when searching for parts to use during an assembly. Composite parts should be documented
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in full detail. While the Registry provides the sequence and annotations from the component parts specified, the function
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<center>'''Make sure to read the FAQ below, before adding parts!'''</center>
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and design issues of the composite part should be documented in detail.<TR><TH align='left' width='25%' style='padding-top: 10px;'>Construction Intermediates
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                <TH align='left'><A href='add_part_ci.cgi'>Add a Construction Intermediate Now...</A><TR><TD  colspan='9' style='padding-left: 15px'>Construction Intermediates have no specific function and are just
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the result of assembling two parts together. They require no further documentation.  They all have the type 'Intermediate'
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<br />
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and part names of the form 'BBa_Snnnnn'. These part names are automatically assigned by the Registry software. Once you
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enter your intermediate part in the Registry, you will be able to use BioBrick Blast to check your assembly's sequence  
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<h3>Basic Parts</h3>
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<a href="https://parts.igem.org/cgi/partsdb/add_part_b.cgi">Add a Basic Part </a>
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<p><a href="https://parts.igem.org/Help:Parts"> Basic Parts </a>  are discrete functional units of DNA: promoters, ribosome binding sites, protein coding regions, etc. They cannot be subdivided into smaller component parts. DNA for a basic part may be obtained by ''de novo'' synthesis, by primer extension and PCR, or via other techniques. <a href="https://parts.igem.org/wiki/index.php/Part:BBa_K863006">BBa_K863006</a> is a good example of a well documented Basic Part. Read <a href="https://parts.igem.org/Help:Adding_Parts">our help page on adding a basic part.</a></p>
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<div style="width:45%; margin:auto; float:left; padding:15px;">
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<h3> Composite Parts</h3>
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<a href="https://parts.igem.org/cgi/partsdb/add_part_c.cgi"> Add a Composite Part </a>
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<p><a href="https://parts.igem.org/Help:Parts">Composite Parts</a> are functional units made from an ordered series of basic parts or other composite parts. <strong>Explicit base pairs of DNA cannot be entered in as sequence for these parts.</strong> The Registry's software provides information and sequence for all the basic parts that you list as components of your composite part. While the Registry provides the sequence from the component parts specified, the function and design issues of the composite part should be documented in detail. <a href="https://parts.igem.org/wiki/index.php/Part:BBa_K1150020">BBa_K1150020</a> is a good example of a well documented Composite Part. Read <a href="https://parts.igem.org/Help:Adding_Parts/Composite"> our help page on adding a composite part</a>.</p>
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<!--
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<h3>Construction Intermediates </h3>
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<a href="https://parts.igem.org/cgi/partsdb/add_part_ci.cgi">Add a Construction Intermediate </a>
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</div>
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<p> Construction Intermediates have no specific function and are just
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the result of assembling two parts together. They require no further documentation.  Often they are unwanted byproducts of construction
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They all have the type 'Intermediate' and part names of the form 'BBa_Snnnnn'. These part names are automatically assigned by the Registry software. Once you enter your intermediate part in the Registry, you will be able to use BioBrick Blast to check your assembly's sequence  
 
and your part will show up in the subpart and superpart search functions. If you send us the DNA, we will be able to share your
 
and your part will show up in the subpart and superpart search functions. If you send us the DNA, we will be able to share your
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work with others and include it in assemblies done by the Registry.
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work with others and include it in assemblies done by the Registry. </p>
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==='''Useful Help Pages'''===
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{{HelpPage/AddingParts}}
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==FAQ==
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{{FAQ/Adding_Parts}}

Latest revision as of 10:38, 4 September 2024

Members of iGEM teams and labs can add two kinds of parts to the Registry: Basic Parts and Composite Parts.


The most important feature of a standard biological part should be that a user of the part does not have to talk to the part's designer. This is achieved by completely documenting the part.


Parts must have a DNA sequence. Registry users should document, model, characterize, and measure their parts, and provide that information on their part pages.

A part can be identified by its DNA sequence, and may be compatible with several Assembly Standards. A sample of a part may be stored in a plasmid backbone that dictates assembly (ex. pSB1C3), and flanked by the prefix and suffix. The prefix and suffix are never included in the sequence of the part when documented on the Registry, as they are a product of the plasmid backbone, and not the part itself. Sample submission of parts is no longer a requirement for the iGEM competition.

Users can add parts to the Registry that adhere to other assembly standards, however BioBrick RFC[10] and Type IIS are the Registry's current de facto standards; all parts on the Registry that will be considered for the iGEM competition (medals, awards, etc.) must be assembly compatible for BioBrick or Type IIS.


Make sure to read the FAQ below, before adding parts!




Basic Parts

Add a Basic Part

Basic Parts are discrete functional units of DNA: promoters, ribosome binding sites, protein coding regions, etc. They cannot be subdivided into smaller component parts. DNA for a basic part may be obtained by ''de novo'' synthesis, by primer extension and PCR, or via other techniques. BBa_K863006 is a good example of a well documented Basic Part. Read our help page on adding a basic part.

Composite Parts

Add a Composite Part

Composite Parts are functional units made from an ordered series of basic parts or other composite parts. Explicit base pairs of DNA cannot be entered in as sequence for these parts. The Registry's software provides information and sequence for all the basic parts that you list as components of your composite part. While the Registry provides the sequence from the component parts specified, the function and design issues of the composite part should be documented in detail. BBa_K1150020 is a good example of a well documented Composite Part. Read our help page on adding a composite part.



Useful Help Pages

Add a Part to the Registry: Related Registry Help Pages
Ready to add your part? Go to the Add a Part page.
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.


FAQ

What's the difference between a basic and composite part?

  • Basic Parts are discrete functional units of DNA. They cannot be subdivided into smaller component parts.
  • Composite Parts are functional units made from an ordered series of basic parts or other composite parts.

In order to create a composite part, each basic part that composes it must already be added and documented to the Registry.


Can I add RNA parts or Proteins (AA)?

No the Registry only accepts DNA. For RNA, you would use the DNA sequence that transcribes your RNA sequence, and give it a part type of RNA.


Tip: Avoid special characters when adding a part

Special characters like ' / - _ in the short description may cause issues with generating the part pages.


How do I delete a part?

You can delete a part by going to a part's "Information" page and setting the DNA status to "deleted".


I synthesized my entire device. Can I add it as a basic part and give it the correct part type?

No, this should be added as a composite part. You should make sure that the basic parts that compose these parts are on the Registry (already exist or you'll be adding them as new basic parts if necessary). You can can go to part tools > edit sequence and features and generate your composite part without BioBrick scars (Blunt Assembly). You can create a small basic part(s) with a part type of "Scar," and enter those in between the basic parts that constitute your composite part.


I want to add a part but do not know the sequence

All users should know their part's sequence before working with it. However, you can still add and document your part and add/edit the sequence later by going to part tools >> edit sequence and features.


How do I document an improvement on an existing part on the Registry?

There are many different ways to improve an existing part, from adding measurement data to codon-optimization. Please see our help page on contributions. Note that the following page is on how to document different types of contributions or improvements. Make sure to read through the medal criteria for a given iGEM year to understand what the judges are looking for.


How do I see if my part is compatible?

The Sequence & Features box will show you assembly compatibility.

The Assembly Compatibility checks that a part will meet the requirements for the Registry's supported assembly standards. It will show if there are any illegal restriction sites for a part. The above image shows a basic part the is compatible with RFC 10 and 1000, amongst others.


Note: All parts submitted to the Registry for competition evaluation (medal criteria, awards) must be BioBrick (RFC[10] compatible or Type IIS RFC[1000], unless an exemption has been given.

See the competition delivearbles page for part requirements


We have a part that we'd like to add, but it is not BioBrick RFC10 compatible or iGEM Type IIS compatible

Yes, please add and document it on the Registry. But make sure to see the parts deliverables page for competition requirements.


Should I include the BioBrick prefix and suffix or iGEM Type IIS prefix and suffix in my part's sequence?

No, your part's sequence should not include the prefix and suffix. While your parts should be assembly compatible, the prefix and suffix are an element of the plasmid backbone, not the part.


How do I upload images to part pages

Use uploads.igem.org to access your upload space. You can then use html tags in the wiki code:

< html ><img src = "url goes here">< /html > (removing the spaces in the html tags)


I have made a part, but cannot edit a wiki page

Make sure to follow the login instructions here, as you need to login to igem.org, and then into the part wiki.